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| | <h3><font style="color:#31B404;">Research</font></h3> |
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| <h3><font style="color:#9ACD32;">Research</font></h3>
| | The Pecinka lab is hosted by the [http://www.mpipz.mpg.de/10574/koornneef-dpt Department of Plant Breeding and Genetics] at the [http://www.mpipz.mpg.de/2169/en Max Planck Institute for Plant Breeding Research] in Cologne, Germany. |
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| The goal of Pecinka lab is to understand molecular basis of mechanisms shaping plant genomes. We focus in particular on DNA repair and inactivation of repetitive DNA that both have potential to cause large genomic chages. To this end we use model species Arabidopsis thaliana and several other Brassicaceae and analyze them using forward and reverse genetics, molecular, biochemical, cytogenetic and bioinformatic methods.
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| Pecinka lab is hosted by the Department of Plant Breeding and Genetics at the Max Planck Institute for Plant Breeding Research in Cologne, Germany.
| | Our goal is to understand molecular and evolutionary mechanisms shaping plant genomes and epigenomes. We analyze how DNA sequence variation is generated by various mutagenic factors and how these forces are counteracted by the genome repair and maintenance mechanisms. To this end we use the model plant ''Arabidopsis thaliana'' and several other ''Brassicaceae'' and analyze them by forward and reverse genetics, molecular, biochemical, cytogenetic and bioinformatic methods. |
| | | [[Pecinka_lab:Research | read more...]] |
| Our wiki site is developed under Openwetware, an open access effort to promote the sharing of information among researchers working in biology.
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| [[Pecinka_Lab:Research | read more...]] | |
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| <h3><font style="color:#4169E1;">Lab Members</font></h3> | | <h3><font style="color:#4169E1;">Lab Members</font></h3> |
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| *[[Pecinka_Lab:Ahmed_Abdelsamad|Ahmed Abdelsamad]] | | *[[Pecinka_lab:Ahmed_Abdelsamad|Ahmed Abdelsamad]] |
| *[[Pecinka_Lab:Chun Hsin Liu|Chun Hsin Liu (Phoebe)]] | | *[[Pecinka_lab:Mariana_Diaz|Mariana Andrea Diaz Smoje]] |
| *[[Pecinka_Lab:Ales_Pecinka|Ales Pecinka]] | | *[[Pecinka_lab:Andreas_Finke|Andreas Finke]] |
| *[[Pecinka_Lab:Björn_Pietzenuk|Björn Pietzenuk]] | | *[[Pecinka_lab:Chun Hsin Liu|Chun Hsin Liu (Phoebe)]] |
| *[[Pecinka_Lab:Thomas_Piofczyk|Thomas Piofczyk]] | | *[[Pecinka_lab:Ales_Pecinka|Ales Pecinka]] |
| *[[Pecinka_Lab:Giang Vu|Giang Vu]]
| | *[[Pecinka_lab:Bjoern_Pietzenuk|Björn Pietzenuk]] |
| | | *[[Pecinka_lab:Thomas_Piofczyk|Thomas Piofczyk]] |
| <h3><font style="color:#4169E1;">Visiting Students</font></h3>
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| *[[Pecinka_Lab:Pawel_Mikulski|Pawel Mikulski]]
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| *[[Pecinka_Lab:Miriam_Schleinitz|Miriam Schleinitz]]
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| <h3><font style="color:#4169E1;">Technitians</font></h3> | | <h3><font style="color:#4169E1;">Technitians</font></h3> |
| *[[Pecinka_Lab:Barbara_Eilts|Barbara_Eilts]] | | *[[Pecinka_lab:Barbara_Eilts|Barbara Eilts]] |
| *[[Pecinka_Lab:Petra_Pecinkova|Petra Pecinkova]] | | *[[Pecinka_lab:Petra_Pecinkova|Petra Pecinkova]] |
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| <h3><font style="color:#4169E1;">Alumni</font></h3>
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| *[[Pecinka_Lab:Alexander Schott|Alexander Schott]]
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| *[[Pecinka_Lab:Anastasia Hoffmann|Anastasia Hoffmann]]
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| [[Pecinka_Lab:Alumni|See all former members...]]
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| <h3><font style="color:#FF8C00;">Recent Publications</font></h3>
| | [[Pecinka_lab:People|see complete list...]] |
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| *Pecinka A, Mittelsten Scheid O (2012): Stress-induced chromatin changes: A critical view on their heritability. Plant Cell Physiology doi: 10.1093/pcp/pcs044. [http://pcp.oxfordjournals.org/content/early/2012/03/28/pcp.pcs044.abstract]
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| *Alcázar R, Pecinka A, Aarts MGM, Fransz PF, Koornneef M (2012): Signals of speciation within Arabidopsis thaliana in comparison with its relatives. Curr Opin Plant Biol 15:205-211. [http://www.sciencedirect.com/science/article/pii/S1369526612000039]
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| *Pecinka A, Fang W, Rehmsmeier M, Levy AA, Mittelsten Scheid O (2011): Polyploidization increases meiotic recombination frequency in Arabidopsis. BMC Biology 9:24. [http://www.biomedcentral.com/1741-7007/9/24]
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| *Pecinka A, Dinh HQ, Rosa M, Baubec T, Lettner N, Mittelsten Scheid O (2010): Epigenetic control of repetitive elements is attenuated by prolonged heat stress in Arabidopsis. Plant Cell 22: 3118–3129. [http://www.plantcell.org/content/22/9/3118.full]
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| *Pecinka A, Rosa M, Schikora A, Berlinger M, Hirt H, Luschnig C, Mittelsten Scheid O (2009): Transgenerational stress memory is not a general response in Arabidopsis. PLoS One 4:e5202. [http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005202]
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| *[[Pecinka_Lab:Publications|see complete list...]]
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| <h3><font style="color:#F8B603;">Announcements</font></h3>
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| *[[Pecinka_Lab:Group_meeting|Group meeting, journal clubs, and seminars]]
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| <h3><font style="color:red">News</font></h3> | | <h3><font style="color:#FF8C00;">Recent Publications</font></h3> |
| *2012-06-07: Pecinka lab page runs on OpenWetWare
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| __NOTOC__
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| | *Piofczyk T, Jeena G, Pecinka A. Arabidopsis thaliana natural variation reveals connections between UV radiation stress and plant pathogen-like defense responses. Plant Physiology Biochemistry DOI: 10.1016/j.plaphy.2015.01.011 (2015) [http://www.sciencedirect.com/science/article/pii/S0981942815000212 Full text] |
| | *Abdelsamad A, Pecinka A. Pollen-Specific Activation of Arabidopsis Retrogenes Is Associated with Global Transcriptional Reprogramming. Plant Cell DOI: http://dx.doi.org/10.1105/tpc.114.126011 (2014). [http://www.plantcell.org/content/early/2014/08/12/tpc.114.126011.full.pdf+html Open access PDF] |
| | *Pecinka A, Liu C.-H. Drugs for Plant Chromosome and Chromatin Research. Cytogenetic Genome Research DOI: 10.1159/000360774 (2014). [http://www.karger.com/Article/FullText/360774 Full text] |
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| <h3><font style="color:#F8B603;">Publications</font></h3>
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| *Kerwin, R. E., Jimenez-Gomez, J. M., Fulop, D., Harmer, S. L., Maloof, J. N. & Kliebenstein, D. J. Network Quantitative Trait Loci Mapping of Circadian Clock Outputs Identifies Metabolic Pathway-to-Clock Linkages in Arabidopsis. Plant Cell 23, 471-485 (2011). [http://dx.doi.org/10.1105/tpc.110.082065] | | *[[Pecinka_lab:Publications|see complete list...]] |
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| *Chang, C. S., Maloof, J. N. & Wu, S. H. COP1-mediated degradation of BBX22/LZF1 optimizes seedling development in Arabidopsis. Plant Physiol (2011). [http://dx.doi.org/10.1104/pp.111.175042]
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| *Nozue, K., Harmer, S. L. & Maloof, J. N. Genomic analysis of circadian clock-, light-, and growth-correlated genes reveals PIF5 as a modulator of auxin signaling in Arabidopsis. Plant Physiol (2011). [http://dx.doi.org/10.1104/pp.111.172684] | | <h3><font style="color:red">News</font></h3> |
| | *2015-02-10: "Arabis alpina" genome reveals peculiar pattern of DNA methylation. See more in the current Nature Plants paper by Schneeberger lab [http://www.nature.com/articles/nplants201423 Full text] |
| | *2015-02-05: Arabidopsis natural variation in response to UV stress reveals connections to pathogen-like responses. Read more in our Plant Physiology and Biochemistry paper [http://www.sciencedirect.com/science/article/pii/S0981942815000212 Full text] |
| | *2014-10-20: Thomas successfully defended his PhD. Congratulations! |
| | *2014-09-22: Lab field trip to Eltz castle. |
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| *Kim, K., Shin, J., Lee, S. H., Kweon, H. S., Maloof, J. N. & Choi, G. Phytochromes inhibit hypocotyl negative gravitropism by regulating the development of endodermal amyloplasts through phytochrome-interacting factors. Proc Natl Acad Sci U S A 108, 1729-1734 (2011). [http://dx.doi.org/10.1073/pnas.1011066108]
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| *Maloof, J. N. Recent advances in regulation of flowering. F1000 Biol Rep 2, (2010). [http://dx.doi.org/10.3410/B2-9]
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| *Brock, M. T., Dechaine, J. M., Iniguez-Luy, F. L., Maloof, J. N., Stinchcombe, J. R. & Weinig, C. Floral Genetic Architecture: An Examination of QTL Architecture Underlying Floral (Co)Variation Across Environments. Genetics 186, 1451-1465 (2010). [http://dx.doi.org/10.1534/genetics.110.119982]
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| *Brock, M. T., Maloof, J. N. & Weinig, C. Genes underlying quantitative variation in ecologically important traits: PIF4 (phytochrome interacting factor 4) is associated with variation in internode length, flowering time, and fruit set in Arabidopsis thaliana. Mol Ecol 19, 1187-1199 (2010). [http://dx.doi.org/10.1111/j.1365-294X.2010.04538.x]
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| *Jiménez-Gómez, J. M., Wallace, A. D. & Maloof, J. N. Network analysis identifies ELF3 as a QTL for the shade avoidance response in Arabidopsis. PLoS Genet 6, (2010). [http://dx.doi.org/10.1371/journal.pgen.1001100]
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| *Jimenez-Gomez, J. M. & Maloof, J. N. Sequence diversity in three tomato species: SNPs, markers, and molecular evolution. BMC Plant Biol 9, 85 (2009). [http://dx.doi.org/10.1186/1471-2229-9-85]
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| *Jiménez-Gómez, J. M. & Maloof, J. N. Plant research accelerates along the (bio)informatics superhighway: symposium on plant sensing, response and adaptation to the environment. EMBO Rep 10, 568-572 (2009). [http://dx.doi.org/10.1038/embor.2009.116]
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| *Schwartz, C., Balasubramanian, S., Warthmann, N., Michael, T. P., Lempe, J., Sureshkumar, S., Kobayashi, Y., Maloof, J. N., Borevitz, J. O., Chory, J. & Weigel, D. Cis-regulatory Changes at FLOWERING LOCUS T Mediate Natural Variation in Flowering Responses of Arabidopsis thaliana. Genetics 183, 723-32, 1SI-7SI (2009). [http://dx.doi.org/10.1534/genetics.109.104984]
| | __NOTOC__ |
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| *Balasubramanian, S., Schwartz, C., Singh, A., Warthmann, N., Kim, M. C., Maloof, J. N., Loudet, O., Trainer, G. T., Dabi, T., Borevitz, J. O., Chory, J. & Weigel, D. QTL Mapping in New Arabidopsis thaliana Advanced Intercross-Recombinant Inbred Lines. PLoS ONE 4, e4318 (2009). [http://dx.doi.org/10.1371/journal.pone.0004318]
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| *Covington, M. F., Maloof, J. N., Straume, M., Kay, S. A. & Harmer, S. L. Global transcriptome analysis reveals circadian regulation of key pathways in plant growth and development. Genome Biol 9, R130 (2008). [http://dx.doi.org/10.1186/gb-2008-9-8-r130]
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| *Filiault, D. L., Wessinger, C. A., Dinneny, J. R., Lutes, J., Borevitz, J. O., Weigel, D., Chory, J. & Maloof, J. N. Amino acid polymorphisms in Arabidopsis phytochrome B cause differential responses to light. Proc Natl Acad Sci U S A 105, 3157-3162 (2008). [http://dx.doi.org/10.1073/pnas.0712174105]
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| *Weinig, C., Johnston, J. A., Willis, C. G. & Maloof, J. N. Antagonistic multilevel selection on size and architecture in variable density settings. Evolution 61, 58-67 (2007). [http://dx.doi.org/10.1111/j.1558-5646.2007.00005.x]
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| *Nozue, K., Covington, M. F., Duek, P. D., Lorrain, S., Fankhauser, C., Harmer, S. L. & Maloof, J. N. Rhythmic growth explained by coincidence between internal and external cues. Nature 448, 358-361 (2007). [http://dx.doi.org/10.1038/nature05946]
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| *Maloof, J. N. Small but not forgotten. Heredity 96, 1-2 (2006). [http://dx.doi.org/10.1038/sj.hdy.6800708]
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| *Balasubramanian, S., Sureshkumar, S., Agrawal, M., Michael, T. P., Wessinger, C., Maloof, J. N., Clark, R., Warthmann, N., Chory, J. & Weigel, D. The PHYTOCHROME C photoreceptor gene mediates natural variation in flowering and growth responses of Arabidopsis thaliana. Nat Genet 38, 711-715 (2006). [http://dx.doi.org/10.1038/ng1818]
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| *Nozue, K. & Maloof, J. N. Diurnal regulation of plant growth. Plant Cell Environ 29, 396-408 (2006).
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| *Lu, L., Lee, Y. R., Pan, R., Maloof, J. N. & Liu, B. An internal motor kinesin is associated with the Golgi apparatus and plays a role in trichome morphogenesis in Arabidopsis. Mol Biol Cell 16, 811-823 (2005). [http://dx.doi.org/10.1091/mbc.E04-05-0400]
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| *Maloof, J. N. Plant development: slowing root growth naturally. Curr Biol 14, R395-R396 (2004). [http://dx.doi.org/10.1016/j.cub.2004.05.016]
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| *Wolyn, D. J., Borevitz, J. O., Loudet, O., Schwartz, C., Maloof, J., Ecker, J. R., Berry, C. C. & Chory, J. Light-response quantitative trait loci identified with composite interval and eXtreme array mapping in Arabidopsis thaliana. Genetics 167, 907-917 (2004). [http://dx.doi.org/10.1534/genetics.103.024810]
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| *Maloof, J. N. Genomic approaches to analyzing natural variation in Arabidopsis thaliana. Curr Opin Genet Dev 13, 576-582 (2003).
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| *Maloof, J. N. QTL for plant growth and morphology. Curr Opin Plant Biol 6, 85-90 (2003).
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| *Nemhauser, J. L., Maloof, J. N. & Chory, J. Building integrated models of plant growth and development. Plant Physiol 132, 436-439 (2003). [http://dx.doi.org/10.1104/pp.102.017061]
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